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[bioontology-support] [BioPortal] Feedback from michelle

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Aug 29 16:39:12 PDT 2017


Hi Michelle,


On Aug 29, 2017, at 2:44 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: michelle

Email: futo at stanford.edu<mailto:futo at stanford.edu>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FFAST-EVENT%3Fp%3Dclasses

Feedback:

I submitted this ontology today https://bioportal.bioontology.org/ontologies/FAST-EVENT/ and I left the default as OWL. Maybe it should have been SKOS. My question is: does that setting (OWL vs SKOS vs OBO etc) change anything about how BioPortal handles the ontology? Wanted to ask this before going to the trouble of submitting it again with SKOS option, and comparing the two.



The formats that BioPortal accepts are OWL, OBO, SKOS, and UMLS. The FAST-EVENT ontology is RDF. The BioPortal user interface doesn’t offer you the option to select RDF as a format since it’s not one of the ones we officially support. I would say it’s not necessary to change the format since the list of available ones doesn’t contain the value that truly reflects the format of the ontology. All ontologies that are submitted via the UI or the REST endpoint are parsed internally using the same software, regardless of the format specified.

The reason that a number of RDF ontologies submitted to BioPortal do end up parsing successfully has to do with how parsing is handled internally. We use 3rd party software to handle the parsing of ontologies called the OWL API [1]. When the OWL API consumes an ontology, it has a number of different parsers it attempts to use to parse the ontology sources. This group of parsers has expanded over the years to include ones that handle RDF. In some cases, RDF ontologies submitted to us will parse, and in other cases, there are difficulties (as you reported with the DCTERMS ontology showing no classes).

The class tree for this ontology appears the same in BioPortal as in the Protege ontology editor, so it appeared to me that this is one case of an RDF ontology that our system handled properly. Unless there was something out of the ordinary you noticed?

Kind regards,
Jennier

[1] https://github.com/owlcs/owlapi/wiki


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